A 30-fold coverage sequence of extinct human relative available through Amazon Web Services

In 2008 scientists discovered a population of premodern humans present in Asia less than 50,000 years ago that were genetically distinct from modern humans and Neanderthals. Svante Pääbo's team described in Nature the complete mitochondrial DNA sequence retrieved from a bone excavated in Denisova Cave in southern Siberia. The sample came from a layer of material that dates from between 30,000 and 50,000 years ago. Interestingly Neanderthal DNA was found in a sample from the same time period less than 100km away, while artifacts indicate that modern humans were also present in the region by 40,000 years ago. While Denisova mtDNA shows about 385 differences with the typical human mitochondrial genome, Neanderthals only differ from modern humans by an average of 202. This indicated that the Denisova lineage split off about a million years ago, well before modern humans and Neanderthals did.

Scientist at the Max Planck Institute have subsequently sequenced the Denisova to about 2 x coverage. Data analysis, published in December 2010 in Nature suggested a more complex picture, with the Denisova population as a sister group to Neanderthals. Differently from Neanderthals, Denisovan ancestors did not contribute genes at a detectable level to present-day people all over Eurasia. However, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. Interestingly, they did not contribute to the genomes of modern asian populations such as Han Chinese and Mongolians which live near Denisova. The Denisovans obviously interbred with the ancestors of modern Melanesians at some point, but it seems unlikely to have happened at Denisova, which suggests that the Denisovans lived over a considerable area of eastern Asia.

Only two days ago the Denisova Genome Consortium released the raw sequence data and alignments for additional sequences generated using the Illumina GAIIx sequencing platform and corresponding to about 30-fold coverage (!!!) of the genome.

Although the researcher are still working on a paper describing their findings, they’ve decided to release the sequence, both on the Max Planck website and through Amazon’s Web Services.

As stated by the authors "the data are available for use, but users are expected to allow the data producers to make the first presentations and to publish the first paper containing genome-wide analyses of the data. Researchers who use small amounts of the data (eg: for single locus analyses) are not required to request permission. Researchers who have queries about whether they may present or submit Denisova genome data for publication may contact Svante Paabo."

It will be interesting to see if the new genomic data will help to shed light on the origin and the fate of Denisovas and their relationship with Neanderthals and modern humans.

In the mean time we can read a nice Nature Reviews Genetics article entitled "Learning about human population history from ancient and modern genomes".